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obitaxonomy: manage and request a taxonomy database
#
Description
#
Synopsis
#
obitaxonomy [--alternative-names|-a] [--batch-size &lt;int&gt;] [--debug]
[--download-ncbi] [--dump|-D &lt;TAXID&gt;] [--extract-taxonomy]
[--fixed|-F] [--force-one-cpu] [--help|-h|-?] [--max-cpu &lt;int&gt;]
[--no-progressbar] [--out|-o &lt;FILENAME&gt;] [--parents|-p &lt;TAXID&gt;]
[--pprof] [--pprof-goroutine &lt;int&gt;] [--pprof-mutex &lt;int&gt;]
[--rank &lt;RANK&gt;] [--rank-list|-l] [--raw-taxid]
[--restrict-to-taxon|-r &lt;string&gt;]... [--solexa]
[--sons|-s &lt;TAXID&gt;] [--taxonomy|-t &lt;string&gt;] [--version]
[--with-path] [--with-query|-P] [--without-parent]
[--without-rank|-R] [--without-scientific-name|-S] [&lt;args&gt;]
Options
#
obitaxonomy
specific options
#
--alternative-names
| -a
: Enable the search on all alternative names and not only scientific names. (default: false)
--download-ncbi: Download the current NCBI taxonomy taxdump (default: false)
--dump
| -D
&lt;TAXID&gt;: Dump a sub-taxonomy corresponding to the precised clade (default: &ldquo;&rdquo;)
--extract-taxonomy: Extract taxonomy from a sequence file (default: false)
--fixed: Match taxon names using a fixed pattern, not a regular expression (default: false)
--parents
| -p
&lt;TAXID&gt;: Displays every parental tree&rsquo;s information for the provided taxid. (default: &ldquo;NA&rdquo;)
--rank &lt;RANK&gt;: Restrict to the given taxonomic rank. (default: &ldquo;&rdquo;)
--rank-list
| -l
: List every taxonomic rank available in the taxonomy. (default: false)
--restrict-to-taxon
| -r
&lt;string&gt;: Restrict output to some subclades. (default: [])
--sons
| -s
&lt;TAXID&gt;: Displays every sons&rsquo; tree&rsquo;s information for the provided taxid. (default: &ldquo;NA&rdquo;)
--with-path: Adds a column containing the full path for each displayed taxon. (default: false)
--with-query
| -P
: Adds a column containing query used to filter taxon name for each displayed taxon. (default: false)
--without-parent: Supress the column containing the parent&rsquo;s taxonid from the output. (default: false)
--without-rank
| -R
: Supress the column containing the taxonomic rank from the output. (default: false)
--without-scientific-name
| -S
: Supress the column containing the scientific name from the output. (default: false)
Taxonomic options
#
--taxonomy
| -t
&lt;string&gt;: Path to the taxonomic database.
General options
#
--help
| -h|-?
: shows this help.
--version: prints the version and exits.
--silent-warning: This option tells obitools to stop displaying warnings.
This behaviour can be controlled by setting the OBIWARNINGS environment variable.
Computation related options
#
--max-cpu &lt;INTEGER&gt;: OBITools can take advantage of your computer&rsquo;s multi-core
architecture by parallelizing the computation across all available CPUs.
Computing on more CPUs usually requires more memory to perform the
computation. Reducing the number of CPUs used to perform a calculation
is also a way to indirectly control the amount of memory used by the
process. The number of CPUs used by OBITools can also be controlled
by setting the OBIMAXCPU environment variable.
--force-one-cpu: forces the use of a single CPU core for parallel processing (default: false).
--batch-size &lt;INTEGER&gt;: number of sequence per batch for parallel processing (default: 1000, env: OBIBATCHSIZE)
Debug related options
#
--debug: enables debug mode, by setting log level to debug (default: false, env: OBIDEBUG)
--pprof: enables pprof server. Look at the log for details. (default: false).
--pprof-mutex &lt;INTEGER&gt;: enables profiling of mutex lock. (default: 10, env: OBIPPROFMUTEX)
--pprof-goroutine &lt;INTEGER&gt;: enables profiling of goroutine blocking profile. (default: 6060, env: OBIPPROFGOROUTINE)
Examples
#
obitaxonomy --help
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<meta property="og:title" content="obitaxonomy">
<meta property="og:description" content="obitaxonomy: manage and request a taxonomy database # Description # Synopsis # obitaxonomy [--alternative-names|-a] [--batch-size &lt;int&gt;] [--debug] [--download-ncbi] [--dump|-D &lt;TAXID&gt;] [--extract-taxonomy] [--fixed|-F] [--force-one-cpu] [--help|-h|-?] [--max-cpu &lt;int&gt;] [--no-progressbar] [--out|-o &lt;FILENAME&gt;] [--parents|-p &lt;TAXID&gt;] [--pprof] [--pprof-goroutine &lt;int&gt;] [--pprof-mutex &lt;int&gt;] [--rank &lt;RANK&gt;] [--rank-list|-l] [--raw-taxid] [--restrict-to-taxon|-r &lt;string&gt;]... [--solexa] [--sons|-s &lt;TAXID&gt;] [--taxonomy|-t &lt;string&gt;] [--version] [--with-path] [--with-query|-P] [--without-parent] [--without-rank|-R] [--without-scientific-name|-S] [&lt;args&gt;] Options # obitaxonomy specific options # --alternative-names | -a : Enable the search on all alternative names and not only scientific names. (default: false) --download-ncbi: Download the current NCBI taxonomy taxdump (default: false) --dump | -D &lt;TAXID&gt;: Dump a sub-taxonomy corresponding to the precised clade (default: “”) --extract-taxonomy: Extract taxonomy from a sequence file (default: false) --fixed: Match taxon names using a fixed pattern, not a regular expression (default: false) --parents | -p &lt;TAXID&gt;: Displays every parental tree’s information for the provided taxid. (default: “NA”) --rank &lt;RANK&gt;: Restrict to the given taxonomic rank. (default: “”) --rank-list | -l : List every taxonomic rank available in the taxonomy. (default: false) --restrict-to-taxon | -r &lt;string&gt;: Restrict output to some subclades. (default: []) --sons | -s &lt;TAXID&gt;: Displays every sons’ tree’s information for the provided taxid. (default: “NA”) --with-path: Adds a column containing the full path for each displayed taxon. (default: false) --with-query | -P : Adds a column containing query used to filter taxon name for each displayed taxon. (default: false) --without-parent: Supress the column containing the parent’s taxonid from the output. (default: false) --without-rank | -R : Supress the column containing the taxonomic rank from the output. (default: false) --without-scientific-name | -S : Supress the column containing the scientific name from the output. (default: false) Taxonomic options # --taxonomy | -t &lt;string&gt;: Path to the taxonomic database. General options # --help | -h|-? : shows this help. --version: prints the version and exits. --silent-warning: This option tells obitools to stop displaying warnings. This behaviour can be controlled by setting the OBIWARNINGS environment variable. Computation related options # --max-cpu &lt;INTEGER&gt;: OBITools can take advantage of your computer’s multi-core architecture by parallelizing the computation across all available CPUs. Computing on more CPUs usually requires more memory to perform the computation. Reducing the number of CPUs used to perform a calculation is also a way to indirectly control the amount of memory used by the process. The number of CPUs used by OBITools can also be controlled by setting the OBIMAXCPU environment variable. --force-one-cpu: forces the use of a single CPU core for parallel processing (default: false). --batch-size &lt;INTEGER&gt;: number of sequence per batch for parallel processing (default: 1000, env: OBIBATCHSIZE) Debug related options # --debug: enables debug mode, by setting log level to debug (default: false, env: OBIDEBUG) --pprof: enables pprof server. Look at the log for details. (default: false). --pprof-mutex &lt;INTEGER&gt;: enables profiling of mutex lock. (default: 10, env: OBIPPROFMUTEX) --pprof-goroutine &lt;INTEGER&gt;: enables profiling of goroutine blocking profile. (default: 6060, env: OBIPPROFGOROUTINE) Examples # obitaxonomy --help">
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<h3>obitaxonomy</h3>
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<li><a href="#obitaxonomy-manage-and-request-a-taxonomy-database"><code>obitaxonomy</code>: manage and request a taxonomy database</a>
<ul>
<li><a href="#description">Description</a></li>
<li><a href="#synopsis">Synopsis</a></li>
<li><a href="#options">Options</a>
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<li></li>
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<article class="markdown book-article"><h1 id="obitaxonomy-manage-and-request-a-taxonomy-database">
<code>obitaxonomy</code>: manage and request a taxonomy database
<a class="anchor" href="#obitaxonomy-manage-and-request-a-taxonomy-database">#</a>
</h1>
<h2 id="description">
Description
<a class="anchor" href="#description">#</a>
</h2>
<h2 id="synopsis">
Synopsis
<a class="anchor" href="#synopsis">#</a>
</h2>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obitaxonomy <span style="color:#f92672">[</span>--alternative-names|-a<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--batch-size &lt;int&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--debug<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--download-ncbi<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--dump|-D &lt;TAXID&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--extract-taxonomy<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--fixed|-F<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--force-one-cpu<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--help|-h|-?<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--max-cpu &lt;int&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--no-progressbar<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--out|-o &lt;FILENAME&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--parents|-p &lt;TAXID&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--pprof<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof-goroutine &lt;int&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--pprof-mutex &lt;int&gt;<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--rank &lt;RANK&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--rank-list|-l<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--raw-taxid<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--restrict-to-taxon|-r &lt;string&gt;<span style="color:#f92672">]</span>... <span style="color:#f92672">[</span>--solexa<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--sons|-s &lt;TAXID&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--taxonomy|-t &lt;string&gt;<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--version<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--with-path<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--with-query|-P<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--without-parent<span style="color:#f92672">]</span>
</span></span><span style="display:flex;"><span> <span style="color:#f92672">[</span>--without-rank|-R<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>--without-scientific-name|-S<span style="color:#f92672">]</span> <span style="color:#f92672">[</span>&lt;args&gt;<span style="color:#f92672">]</span>
</span></span></code></pre></div><h2 id="options">
Options
<a class="anchor" href="#options">#</a>
</h2>
<h4 id="hahahugoshortcode41s0hbhb-specific-options">
<a href="http://metabar:8888/obidoc/obitools/obitaxonomy/">
<abbr title="obitaxonomy: manage and search in the taxonomic database"><code>obitaxonomy</code></abbr>
</a> specific options
<a class="anchor" href="#hahahugoshortcode41s0hbhb-specific-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--alternative-names</code></b>
| <b><code class="language-bash">-a</code></b>
: Enable the search on all alternative names and not only scientific names. (default: false)</li>
<li><b><code class="language-bash">--download-ncbi</code></b>: Download the current NCBI taxonomy taxdump (default: false)</li>
<li><b><code class="language-bash">--dump</code></b>
| <b><code class="language-bash">-D</code></b>
&lt;TAXID>: Dump a sub-taxonomy corresponding to the precised clade (default: &ldquo;&rdquo;)</li>
<li><b><code class="language-bash">--extract-taxonomy</code></b>: Extract taxonomy from a sequence file (default: false)</li>
<li><b><code class="language-bash">--fixed</code></b>: Match taxon names using a fixed pattern, not a regular expression (default: false)</li>
<li><b><code class="language-bash">--parents</code></b>
| <b><code class="language-bash">-p</code></b>
&lt;TAXID>: Displays every parental tree&rsquo;s information for the provided taxid. (default: &ldquo;NA&rdquo;)</li>
<li><b><code class="language-bash">--rank</code></b> &lt;RANK>: Restrict to the given taxonomic rank. (default: &ldquo;&rdquo;)</li>
<li><b><code class="language-bash">--rank-list</code></b>
| <b><code class="language-bash">-l</code></b>
: List every taxonomic rank available in the taxonomy. (default: false)</li>
<li><b><code class="language-bash">--restrict-to-taxon</code></b>
| <b><code class="language-bash">-r</code></b>
&lt;string>: Restrict output to some subclades. (default: [])</li>
<li><b><code class="language-bash">--sons</code></b>
| <b><code class="language-bash">-s</code></b>
&lt;TAXID>: Displays every sons&rsquo; tree&rsquo;s information for the provided taxid. (default: &ldquo;NA&rdquo;)</li>
<li><b><code class="language-bash">--with-path</code></b>: Adds a column containing the full path for each displayed taxon. (default: false)</li>
<li><b><code class="language-bash">--with-query</code></b>
| <b><code class="language-bash">-P</code></b>
: Adds a column containing query used to filter taxon name for each displayed taxon. (default: false)</li>
<li><b><code class="language-bash">--without-parent</code></b>: Supress the column containing the parent&rsquo;s taxonid from the output. (default: false)</li>
<li><b><code class="language-bash">--without-rank</code></b>
| <b><code class="language-bash">-R</code></b>
: Supress the column containing the taxonomic rank from the output. (default: false)</li>
<li><b><code class="language-bash">--without-scientific-name</code></b>
| <b><code class="language-bash">-S</code></b>
: Supress the column containing the scientific name from the output. (default: false)</li>
</ul>
<h4 id="taxonomic-options">
Taxonomic options
<a class="anchor" href="#taxonomic-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--taxonomy</code></b>
| <b><code class="language-bash">-t</code></b>
&lt;string>: Path to the taxonomic database.
</li>
</ul>
<h4 id="general-options">
General options
<a class="anchor" href="#general-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--help</code></b>
| <b><code class="language-bash">-h|-?</code></b>
: shows this help.</li>
<li><b><code class="language-bash">--version</code></b>: prints the version and exits.</li>
<li><b><code class="language-bash">--silent-warning</code></b>: This option tells obitools to stop displaying warnings.
This behaviour can be controlled by setting the <strong>OBIWARNINGS</strong> environment variable.</li>
</ul>
<h4 id="computation-related-options">
Computation related options
<a class="anchor" href="#computation-related-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--max-cpu</code></b> &lt;INTEGER>: <em>OBITools</em> can take advantage of your computer&rsquo;s multi-core
architecture by parallelizing the computation across all available CPUs.
Computing on more CPUs usually requires more memory to perform the
computation. Reducing the number of CPUs used to perform a calculation
is also a way to indirectly control the amount of memory used by the
process. The number of CPUs used by <em>OBITools</em> can also be controlled
by setting the <strong>OBIMAXCPU</strong> environment variable.</li>
<li><b><code class="language-bash">--force-one-cpu</code></b>: forces the use of a single CPU core for parallel processing (default: false).</li>
<li><b><code class="language-bash">--batch-size</code></b> &lt;INTEGER>: number of sequence per batch for parallel processing (default: 1000, env: <strong>OBIBATCHSIZE</strong>)</li>
</ul>
<h4 id="debug-related-options">
Debug related options
<a class="anchor" href="#debug-related-options">#</a>
</h4>
<ul>
<li><b><code class="language-bash">--debug</code></b>: enables debug mode, by setting log level to debug (default: false, env: <strong>OBIDEBUG</strong>)</li>
<li><b><code class="language-bash">--pprof</code></b>: enables pprof server. Look at the log for details. (default: false).</li>
<li><b><code class="language-bash">--pprof-mutex</code></b> &lt;INTEGER>: enables profiling of mutex lock. (default: 10, env: <strong>OBIPPROFMUTEX</strong>)</li>
<li><b><code class="language-bash">--pprof-goroutine</code></b> &lt;INTEGER>: enables profiling of goroutine blocking profile. (default: 6060, env: <strong>OBIPPROFGOROUTINE</strong>)</li>
</ul>
<h2 id="examples">
Examples
<a class="anchor" href="#examples">#</a>
</h2>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obitaxonomy --help
</span></span></code></pre></div></article>
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<li><a href="#obitaxonomy-manage-and-request-a-taxonomy-database"><code>obitaxonomy</code>: manage and request a taxonomy database</a>
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